MolNFT v1 · #99143 · protein
Alanine racemase [clostridium difficile 630] complex with cycloserine
4LUT: “Alanine racemase [clostridium difficile 630] complex with cycloserine”. X-ray diffraction, 1 ligand (DCS), 9 pockets (best druggability 0.81). MolNFT v1 #99143 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4LUT
- Type
- protein
- Length
- 739 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase
- EC
- 5.1.1.1
- UniProt
- Q180W0
- Ligands
- DCS
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine racemase (EC 5.1.1.1) | protein | 375 | 34% helix, 26% strand | Q180W0 |
| B | Alanine racemase (EC 5.1.1.1) | protein | 364 | 34% helix, 26% strand | Q180W0 |
Ligands and binding sites
- DCS · D-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-N,O-cycloserylamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.81 | 0.96 | 44 | empty |
| 2 | 872 | 0.76 | 0.79 | 78 | DCS |
| 3 | 362 | 0.75 | 0.86 | 57 | DCS |
| 4 | 61 | 0.53 | 0.87 | 20 | empty |
| 5 | 66 | 0.41 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2887 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (carboxylation).
Compared structures
- 4LUT · alanine racemase [Clostridium difficile 630] complex with cycloserine · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q180W0
- Elsewhere: RCSB PDB 4LUT · PDBe 4LUT · UniProt Q180W0
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